Modules:FetchMI-Documentation-3.4

Return to Slicer 3.4 Documentation

Module Name

Fetch Medical Informatics (FetchMI)

SPL Abdominal Atlas on xnd.slicer.org

SPL Brain Atlas on xnd.slicer.org

Registration tutorial data on xnd.slicer.org

General Information

Module Type & Category

Type: Interactive

Category: Informatics

Authors, Collaborators & Contact

• Author1: Wendy Plesniak
• Contributor1: Nicole Aucoin
• Contributor2: Steve Pieper
• Contact: Wendy Plesniak, wjp@bwh.harvard.edu

Module Description

FetchMI (Fetch Medical Informatics) is a 'sandbox' functionality being developed to remotely upload, download and tag Slicer scenes and datasets. Its functionality will eventually be moved into Slicer's base code (into the load and save panels) and into a separate module for data markup. Currently, FetchMI interoperates with XNAT Desktop's web services. Its functionality is being extended to work with BIRN's HID and XNAT Enterprise web services.

The module can be used to browse remote repositories for data, download MRML scenes into Slicer, associate metadata with loaded data and the scene description, and upload a scene and its referenced data to a remote host. The interface also permits remote deleting of MRML scenes and their referenced resources.

Usage

Examples, Use Cases & Tutorials

• Note use cases for which this module is especially appropriate, and/or link to examples.
• Download XNAT Desktop
• Link to XNAT Desktop tutorial

Brief instruction

• Select a server. All subsequent operations will transact with the selected server.
• The selected server will automatically be queried for the metadata it currently supports. The panel in the Query for Scenes tab will be populated with this metadata (attributes and available values). Update this panel time by clicking the Refresh button.
• Select any tags you want to use to query for resources
• Click the Search button (binoculars) to query the server for matching resources.
• The Browse Query Results & Download tab will be populated by a list of resources matching the query.
• Select a resource (MRML Scenes only) from that list.
• Click the Download button and the scene will be downloaded to your current cache directory and loaded.
• The Tag Scene & Upload tab shows all data in scene (and scene file).
• Select or create new tags using the menubutton at the top of this panel, and click the Apply Tags button to associate to selected datasets. Click the Remove Tags button to dissociate selected tag from selected datasets.
• NOTE: tags should be brief. At this time, tags CANNOT include SPACES or any special characters; we will admit these options in future development.
• Click the Show All Tags button to see all tags on all loaded datasets and scene.
• Upload the current scene to the server by clicking the Upload button, after data is tagged. In this version, the entire scene and all datasets are uploaded.
• NOTE: remote uploads and downloads can be slow. Though we have attempted to construct safeguards, Initiating these without access to the network or without access to the selected server may still lead to unexpected application behavior. Please report any unexpected behavior to Slicer's bug tracker.

Quick Tour of Features and Use

Below is a tour of interfaces to FetchMI's functionality, with explanatory information and suggestions for use:

• Select a web service:

• Query for Scenes tab:

• Browse Query Results & Download tab:

• Tag Scene & Upload tab:

Development

Dependencies

Other modules or packages that are required for this module's use.

Known bugs

Follow this link to the Slicer3 bug tracker.

Usability issues

Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.

Source code & documentation

Customize following links for your module.

Links to documentation generated by doxygen.

More Information

Acknowledgment

Include funding and other support here.

References

Publications related to this module go here. Links to pdfs would be useful.